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[MRG] Improve cell classes #322

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merged 49 commits into from May 6, 2021
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a430ee9
MAINT: Unify set_geometry
jasmainak Apr 29, 2021
ff26c15
ENH: more simplification
jasmainak Apr 29, 2021
79807f6
ENH: Unify more
jasmainak Apr 29, 2021
af0f6ed
More compact?
jasmainak Apr 29, 2021
460161e
WIP: improvement or not?
jasmainak Apr 29, 2021
b34bb1c
MAINT: make class thinner
jasmainak Apr 29, 2021
1c08f18
MAINT: simplify
jasmainak Apr 29, 2021
37bd4a6
ENH: simplify more
jasmainak Apr 29, 2021
a0c81eb
MAINT: no need of list_dend
jasmainak Apr 29, 2021
ff76f20
ENH: set_biophysics in parent class
jasmainak Apr 29, 2021
ad48927
MAINT: move cell classes to one file
jasmainak Apr 29, 2021
6f2a43b
ENH: Remove superfluous celltype
jasmainak Apr 29, 2021
49c4b96
self.L and self.diam not needed
jasmainak Apr 29, 2021
5952a1b
MAINT: l2_basket and l5_basket into func
jasmainak Apr 29, 2021
22e4a4b
ENH: remove BasketSingle
jasmainak Apr 30, 2021
d3631ec
Move set_biophysics to init
jasmainak Apr 30, 2021
7a989f8
No more L2Pyr and L5Pyr
jasmainak Apr 30, 2021
0efbbc1
MAINT: more reorganization. Don't create soma on cell init
jasmainak Apr 30, 2021
cb09a5c
ENH: move pos out of soma_props
jasmainak Apr 30, 2021
3839f1e
ENH: move create_dends to parent class
jasmainak Apr 30, 2021
3b951eb
ENH: cell shouldn't take soma_props as argument
jasmainak Apr 30, 2021
759f22a
MAINT: remove another method
jasmainak Apr 30, 2021
58dbe27
Mechanism by section
jasmainak May 1, 2021
6f3f7d4
Better name
jasmainak May 1, 2021
a8fa99b
MAINT: get rid of set_geometry too
jasmainak May 1, 2021
bf21816
Last method gone
jasmainak May 1, 2021
ce242dd
Pyr becomes function
jasmainak May 1, 2021
9e19f23
ENH: simplify?
jasmainak May 1, 2021
76f0dd6
Introduce p_secs. Must make a class later
jasmainak May 1, 2021
b47acf9
Cosmit: p_secs first, then Neuron code
jasmainak May 2, 2021
1c9b6f3
ENH: introduce cell.build
jasmainak May 2, 2021
381983b
p_dend should be updated after default geometry is set
jasmainak May 3, 2021
e601798
ENH: simplify
jasmainak May 3, 2021
e6e2c3c
ENH: compress into single method create_sections
jasmainak May 3, 2021
f79a157
FIX: address comments by chris
jasmainak May 3, 2021
0ab24a8
ENH: bit more simplification
jasmainak May 3, 2021
f15693d
ENH: allow callable in mech value
jasmainak May 4, 2021
d2a671d
DOC: better documentation
jasmainak May 4, 2021
7a2fa56
ENH: rename cell_classes to cells_default.py
jasmainak May 4, 2021
9fd39bc
MAINT: more failsafe connection of sections
jasmainak May 4, 2021
bb763cf
MAINT: no more self.secs
jasmainak May 4, 2021
4958167
ENH: sec_pts is documented + sect_loc is updated transparently?
jasmainak May 4, 2021
2ff530f
FIX some quick fixes
jasmainak May 5, 2021
9557f02
MAINT: unify celltype, cell_type, and cell_name
jasmainak May 5, 2021
cefc434
Clearer code?
jasmainak May 5, 2021
6b76eec
MAINT: get rid of self.soma
jasmainak May 5, 2021
5d38fec
TST: add tests for cell class
jasmainak May 5, 2021
abac3b2
TST: some basic tests for default cell type
jasmainak May 5, 2021
1ee4a93
ENH: address ryan comments + simplification
jasmainak May 5, 2021
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5 changes: 1 addition & 4 deletions doc/api.rst
Expand Up @@ -14,12 +14,9 @@ Simulation (:py:mod:`hnn_core`):
.. autosummary::
:toctree: generated/

L2Pyr
L5Pyr
L2Basket
L5Basket
simulate_dipole
Network
Cell
CellResponse

Dipole (:py:mod:`hnn_core.dipole`):
Expand Down
3 changes: 1 addition & 2 deletions hnn_core/__init__.py
Expand Up @@ -3,8 +3,7 @@
from .params import Params, read_params
from .network import Network
from .cell_response import CellResponse, read_spikes
from .pyramidal import L2Pyr, L5Pyr
from .basket import L2Basket, L5Basket
from .cells_default import pyramidal, basket
from .parallel_backends import MPIBackend, JoblibBackend

__version__ = '0.2.dev0'
125 changes: 0 additions & 125 deletions hnn_core/basket.py

This file was deleted.